Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_014034	2,747,876	2 bp→GC	100%	intergenic (‑208/+84)	RCAP_rcc02553 ← / ← RCAP_rcc02554	hypothetical protein/NmrA family protein

Read alignment evidence...
	seq id	position		change	freq	score	reads	annotation	genes	product
*	NC_014034	2,747,876	0	C→G	100.0%	133.7	52	intergenic (‑208/+85)	RCAP_rcc02553/RCAP_rcc02554	hypothetical protein/NmrA family protein
Reads supporting (aligned to +/- strand):  new base (47/5):  ref base (0/0):  total (47/5)
*	NC_014034	2,747,877	0	T→C	100.0%	187.2	66	intergenic (‑209/+84)	RCAP_rcc02553/RCAP_rcc02554	hypothetical protein/NmrA family protein
Reads supporting (aligned to +/- strand):  new base (58/8):  ref base (0/0):  total (58/8)

GCCCGCAGCGCCCGGTTGCGGCATGACCGCTTCAGCCCGCACCACAGAGGGCAGCGCCCGGCCC.GCGGCCGAGAAGCGCCCGC.C.GGCCGGCTGCTGCCCGAGGGCCTTTGGGCCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATGGCCTTGGCCAAGGTCAGCTCATGCCAGCG  >  NC_014034/2747786‑2747971                                                                                              ||                                                                                               gcccgcAGCGCCCGGTTGCGGCATGACCGCTTCAGCCCGCACCACAGAGGGCAGCGCCCGGCCCGGCGGGCGAGAAGCGCCCGC.CGGGCCGGGCGCTGccc                                                                                         >  2:3176145/1‑101 (MQ=21)      cAGCGCCCGGTTGCGGCATGACCGCTTCAGCCCGCACCACAGAGGGCAGCGCCCGGCCCGGCGGGCGAGAAGCGCCCGC.CGGGCCGGGCGCTGCCCGAggg                                                                                    >  1:2181087/1‑101 (MQ=21)      cAGCGCCCGGTTGCGGCATGACCGCTTCAGCCCGCACCACAGAGGGCAGCGCCCGGCCCGGCGGGCGAGAAGCGCCCGC.CGGGCCGGGCGCTGCCCGAggg                                                                                    >  1:6985203/1‑101 (MQ=21)              ggTTGCGGCATGACCGCTTCAGCCCGCACCACAGAGGGCAGCGCCCGGCCCGGCGGGCGAGAAGCGCCCGC.CGGGCCGGGCGCTGCCCGAGGGCCTTTggg                                                                            >  2:105242/1‑101 (MQ=21)               gTTGCGGCATGACCGCTTCAGCCCGCACCACAGAGGGCAGCGCCCGGCCCGGCGGGCGAGAAGCGCCCGC.CGGGCCGGGCGCTGCCCGAGGGCCTTTGGGc                                                                           >  1:1352811/1‑101 (MQ=18)                tggCGCCATGACCGCTTCCGCCCGCCCCACAGAGGGCAGCGCCCGGCCCGGCGGGCGAGAAGCGCCCGC.CGGGCCGGGCGCTGCCTGAGGGCCTTCGGGcc                                                                          <  1:8848461/99‑1 (MQ=12)                         gACCGCTTCAGCCCGCACCACAGAGGGCAGCGCCCGGCCCGGCGGGCGAGAAGCGCCCGC.CGGGCCGGGCGCTGCCCGAGGGCCTTTGGGCCCTCgggggg                                                                 >  2:163826/1‑100 (MQ=17)                         gACCGCTTCAGCCCGCACCACAGAGGGCAGCGCCCGGCCCGGCGGGCGAGAAGCGCCCGC.CGGGCCGGGCGCTGCCCGAGGGCCTTTGGGCCCTCGGGGGt                                                                 >  2:8220228/1‑101 (MQ=17)                           ccGCTTCAGCCCGCACCACAGAGGGCAGCGCCCGGCCCGGCGGGCGAGAAGCGCCCGC.CGGGCCGGGCGCTGCCCGAGGGCCTTTGGGCCCTCGGGGGTcg                                                               >  1:5674361/1‑100 (MQ=17)                                   gCCCGCACCACAGGGGGCAGCGCCCGGCCCGGCGGGCGAGAAGCGCCCGC.CGGGCCGGGCGCTGCCCGAGGGCCTTTGGGCCCTCGGGGGTCACAGGACct                                                       <  2:6711802/101‑1 (MQ=17)                                            acaGAGGGCAGCGCCCGGCCCGGCGGGCGAGAAGCGCCCGC.CGGGCCGGGCGCTGCCCGAGGGCCTTTGGGCCCTCGGGGGGCACAGGACCTCTGTGACGc                                              >  1:2809451/1‑101 (MQ=14)                                              agagGGCAGCGCCCGGCCCGGCGGGCGAGAAGCGCCCGC.CGGGCCGGGCGCTGCCCGCGGGCCCTTGGGACCTCGGGGGGCACAGGACctcgctgaaccat                                            >  2:5602623/1‑91 (MQ=9)                                                agGGCAGCGCCCGGCCCGGCGGGCGAGAAGCGCCCGC.CGGGCCGGGCGCTGCCCGAGGGCCTTTGGGCCCTCGGGGGTCACCGGACCTCTGTGACGCATgg                                          >  1:404067/1‑101 (MQ=17)                                                  ggCAGCGCCCGGCCCGGCGGGCGAGAAGCGCCCGC.CGGGCCGGGCGCTGCCCGAGGGCCTTTGGGCCCTCGGGGGTCACAGGACCTCTGTGACGCATGGcc                                        <  1:5292657/101‑1 (MQ=18)                                                     aGCGCCCGGCCCGGCGGGCGAGAAGCGCCCGC.CGGGCCGGGCGCTGCCCGAGGGCCTTTGGGCCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAg                                     >  2:3899231/1‑101 (MQ=18)                                                        gcccggcccgGCGGGCGAGAAGCGCCCGC.CGGGCCGGGCGCTGCCCGAGGGCCTTTGGGCCCTCGGGGGGCACAGGACCTCTGTGACGCATGGCCAAGGCg                                  >  2:1312199/1‑101 (MQ=18)                                                          ccggcccgGCGGGCGAGAAGCGCCCGC.CGGGCCGGGCGCTGCCCGAGGGCCTTTGGGCCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGAt                                >  2:8867149/1‑101 (MQ=18)                                                           cggcccgGCGGGCGAGAAGCGCCCGC.CGGGCCGGGCGCTGCCCGAGGGCCTTTGGGCCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATg                               >  2:6063818/1‑101 (MQ=18)                                                           cggcccgGCGGGCGAGAAGCGCCCGC.CGGGCCGGGCGCTGCCCGAGGGCCTTTGGGCCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATg                               >  1:6415860/1‑101 (MQ=18)                                                            ggcccgGCGGGCGAGAAGCGCCCGC.CGGGCCGGGCGCTGCCCGAGGGCCTTTGGGCCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATgg                              >  2:4308773/1‑101 (MQ=18)                                                            ggcccgGCGGGCGAGAAGCGCCCGC.CGGGCCGGGCGCTGCCCGAGGGCCTTTGGGCCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATgg                              >  2:4722952/1‑101 (MQ=18)                                                            ggcccgGCGGGCGAGAAGCGCCCGC.CGGGCCGGGCGCTGCCCGAGGGCCTTTGGGCCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATgg                              >  1:6819173/1‑101 (MQ=18)                                                              cccggcgGGCGAGAAGCGCCCGC.CGGGCCGGGCGCTGCCCGAGGGCCTTTGGGCCCTCGGGGGTCACAGGACCTCTGTGACGCCTGGCCAAGGCGATGGcc                            >  2:5370381/5‑101 (MQ=18)                                                               ccggcgGGCGAGAAGCGCCCGC.CGGGCCGGGCGCTGCCCGAGGGCCTTTGGGCCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATGGCCt                           >  1:8779012/4‑101 (MQ=21)                                                                cggcgGGCGAGAAGCGCCCGC.CGGGCCGGGCGCTGCCCGAGGGCCTTTGGGCCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATGGCCtt                          >  2:1211984/3‑101 (MQ=21)                                                                 ggggggcGAGAACCGCCCGC.CGGGCCGGGCGCTGCCCGAGGGCCTTTGGGCCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATGGCCTTg                         <  2:2181025/95‑1 (MQ=25)                                                                 ggcgGGCGAGAAGCGCCCGC.CGGGCCGGGCGCTGCCCGAGGGCCTTTGGGCCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATGGCCTTg                         >  2:3722908/2‑101 (MQ=21)                                                                 ggcgGGCGAGAAGCGCCCGC.CGGGCCGGGCGCTGCCCGAGGGCCTTTGGGCCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATGGCCTTg                         >  1:8537440/2‑101 (MQ=21)                                                                  gcgGGCGAGAAGCGCCCGC.CGGGCCGGGCGCTGCCCGAGGGCCTTTGGGCCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATGGCCTTgg                        >  2:5583178/1‑101 (MQ=21)                                                                   cgGGCGAGAAGCGCCCGC.CGGGCCGGGCGCTGCCCGAGGGCCTTTGGGCCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATGGCCTTGGc                       >  1:4873770/1‑101 (MQ=21)                                                                   cgGGCGAGAAGCGCCCGC.CGGGCCGGGCGCTGCCCGAGGGCCTTTGGGCCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATGGCCTTGGc                       >  1:4959886/1‑101 (MQ=21)                                                                   cgGGCGAGAAGCGCCCGC.CGGGCCGGGCGCTGCCCGAGGGCCTTTGGGCCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATGGCCTTGGc                       >  2:3511875/1‑101 (MQ=21)                                                                   cgGGCGAGAAGCGCCCGC.CGGGCCGGGCGCTGCCCGAGGGCCTTTGGGCCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATGGCCTCGGc                       >  1:7856920/1‑101 (MQ=18)                                                                    ggtcGAGAGGCGCCCGC.CGGGCCGGGCGCGGCCCGAGGGCCTTTGGGCCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATGGCCTTGGcc                      <  1:4250290/98‑1 (MQ=21)                                                                    gggcGAGAAGCGCCCGC.CGGGCCGGGCGCTGCCCGAGGGCCTTTGGGCCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATGGCCTTGGcc                      >  1:55928/4‑101 (MQ=21)                                                                    gggcGAGAAGCGCCCGC.CGGGCCGGGCGCTGCCCGAGGGCCTTTGGGCCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATGGCCTTGGcc                      >  1:5151630/4‑101 (MQ=21)                                                                     ggcGAGAAGCGCCCGC.CGGGCCGGGCGCTGCCCGAGGGCCTTTGGGCCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATGGCCTTGGCCa                     >  2:3533190/3‑101 (MQ=21)                                                                      gcGAGGAGCGCCCGCGG.GGCCGGGCGCTGCCCGAGGGCCTTTGGGCCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATGGCCTTGGCCaa                    >  1:8839980/2‑101 (MQ=18)                                                                      gcGAGAAGCGCCCGC.CGGGCCGGGCGCTGCCCGAGGGCCTTTGGGCCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATGGCCTTGGCCaa                    >  2:7875370/2‑101 (MQ=21)                                                                       cGAGAAGCGCCCGC.CGGGCCGGGCGCTGCCCGAGGGCCTTTGGGCCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATGGCCTTGGCCAAg                   >  2:5294380/1‑101 (MQ=21)                                                                        gagaAGCGCCCGC.CGGGCCGGGCGCTGCCCGAGGGCCTTTGGGCCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATGGCCTTGGCCAAgg                  >  1:5904015/1‑101 (MQ=21)                                                                        gagaAGCGCCCGC.CGGGCCGGGCGCTGCCCGAGGGCCTTTGGGCCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATGGCCTTGGCCAAgg                  >  1:1185828/1‑101 (MQ=21)                                                                        gagaAGCGCCCGC.CGGGCCGGGCGCTGCCCGAGGGCCTTTGGGCCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATGGCCTTGGCCAAga                  >  1:4981301/1‑100 (MQ=21)                                                                         agaAGCGCCCGC.CGGGCCGGGCGCTGCCCGCGGGCCTTTGGGCCCTCGGGGGTCCCCGGACCTCTGTGACGCATGGCCCAGGCGCTCGCCTTGGCCACggc                 >  2:8134864/1‑100 (MQ=18)                                                                         agaAGCGCCCGC.CGGGCCGGGCGCTGCCCGAGGGCCTTTGGGCCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATGGCCTTGGCCAAggg                 >  1:8469820/1‑100 (MQ=21)                                                                         agaAGCGCCCGC.CGGGCCGGGCGCTGCCCGAGGGCCTTTGGGCCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATGGCCTTGGCCAAGGt                 >  2:5188832/1‑101 (MQ=21)                                                                         agaAGCGCCCGC.CGGGCCGGGCGCTGCCCGAGGGCCTTTGGGCCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATGGCCTTGGCCAAGGt                 >  2:2305375/1‑101 (MQ=21)                                                                         agaAGCGCCCGC.CGGGCCGGGCGCTGCCCGAGGGCCTTTGGGCCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATGGCCTTGGCCAAGGt                 >  1:8713518/1‑101 (MQ=21)                                                                          gaAGCGCCCGC.CGGGCCGGGCGCTGCCCGAGGGCCTTTGGGCCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATGGCCTTGGGCAAggga                >  2:4856809/1‑99 (MQ=21)                                                                          gaAGCGCCCGC.CGGGCCGGGCGCTGCCCGAGGGCCTTTGGGCCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATGGCCTTGGCCAAGGTc                >  2:5080740/1‑101 (MQ=21)                                                                          gaAGCGCCCGC.CGGGCCGGGCGCTGCCCGAGGGCCTTTGGGCCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATGGCCTTGGCCAAGGTc                >  2:8919093/1‑101 (MQ=21)                                                                           aaGCGCCCGC.CGGGCCGGGCGCTGCCCGAGGGCCTTTGGGCCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATGGCCTTGGCCAAGGTCa               >  2:7650153/1‑101 (MQ=21)                                                                            aGCGCCCGC.CGGGCCGGGCGCTGCCCGAGGGCCTTTGGGCCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATGGCCTTGGCCAAGGTCAg              >  1:1524597/1‑101 (MQ=21)                                                                             gcgcCCGC.CGGGCCGGGCGCTGCCCGAGGGCCTTTGGGCCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATGGCCTTGGCCAAGGTCAGc             >  1:1163668/1‑101 (MQ=21)                                                                                gcccggcgggccgggCGCTGCCCGAGGGCCTTTGGGCCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATGGCCTTGGCCAAGGCCAGccc           >  2:4527948/9‑99 (MQ=18)                                                                                   cgccgggccgggCGCTGCCCGAGGGCCTTTGGGCCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATGGCCTTGGCCAAGGTCAGCTCATg        >  2:6038502/6‑101 (MQ=255)                                                                                    gccgggccgggCGCTGCCCGAGGGCCTTTGGGCCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATGGCCTTGGCCAAGGTCAGCTCATGc       >  1:5821698/5‑101 (MQ=255)                                                                                    gccgggccgggCGCTGCCCGAGGGCCTTTGGGCCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATGGCCTTGGCCAAGGTCAGCTCATGc       >  1:2820766/5‑101 (MQ=255)                                                                                     ccgggccgggCGCTGCCCGAGGGCCTTTGGGCCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATGGCCTTGGCCAAGGTCAGCTCATGcc      >  2:7235007/4‑101 (MQ=255)                                                                                     ccgggccgggCGCTGCCCGAGGGCCTTTGGGCCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATGGCCTTGGCCAAGGTCAGCTCATGcc      <  1:5602830/98‑1 (MQ=255)                                                                                      cgggccgggCGCTGCCCGAGGGCCTTTGGGCCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATGGCCTTGGCCAAGGTCAGCTCATGCCa     >  2:5888360/3‑101 (MQ=255)                                                                                      cgggccgggCGCTGCCCGAGGGCCTTTGGGCCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATGGCCTTGGCCAAGGTCAGCTCATGCCa     >  1:5650651/3‑101 (MQ=255)                                                                                       gggccgggCGCTGCCCGAGGGCCTTTGGGCCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATGGCCTTGGCCAAGGTCAGCTCATGCCAg    >  2:4935038/2‑101 (MQ=255)                                                                                       gggccgggCGCTGCCCGAGGGCCTTTGGGCCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATGGCCTTGGCCAAGGTCAGCTCATGCCAg    <  2:4394002/100‑1 (MQ=255)                                                                                       gggccgggCGCTGCCCGAGGGCCTTTGGGCCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATGGCCTTGGCCAAGGTCAGCTCATGCCAg    >  2:7091124/2‑101 (MQ=255)                                                                                        ggccgggCGCTGCCCGAGGGCCTTTGGGCCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATGGCCTTGGCCAAGGTCAGCTCATGCCAgc   <  2:1352779/101‑1 (MQ=255)                                                                                         gccgggCGCTGCCCGAGGGCCTTTGGGCCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATGGCCTTGGCCAAGGTCAGCTCATGCCAgcg  >  2:6001696/1‑101 (MQ=255)                                                                                         gccgggCGCTGCCCGAGGGCCTTTGGGCCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATGGCCTTGGCCAAGGTCAGCTCATGCCAgcg  >  1:1503780/1‑101 (MQ=255)                                                                                              ||                                                                                               GCCCGCAGCGCCCGGTTGCGGCATGACCGCTTCAGCCCGCACCACAGAGGGCAGCGCCCGGCCC.GCGGCCGAGAAGCGCCCGC.C.GGCCGGCTGCTGCCCGAGGGCCTTTGGGCCCTCGGGGGTCACAGGACCTCTGTGACGCATGGCCAAGGCGATGGCCTTGGCCAAGGTCAGCTCATGCCAGCG  >  NC_014034/2747786‑2747971 Base quality scores:  ATCG  < 3 ≤  ATCG  < 18 ≤  ATCG  < 27 ≤  ATCG  < 33 ≤  ATCG  < 40 ≤  ATCG